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Intro to Data Analysis

Utah Valley University - BIOL3100

Quick links:

Course GitHub Repository

Course Syllabus

Shared Course Notes

(Anyone with link can edit)

The philosophy of this course

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Table of Contents

Week 1 | Week 5 | Week 9 | Week 13

Week 2 | Week 6 | Week 10 | Week 14

Week 3 | Week 7 | Week 11 | Week 15

Week 4 | Week 8 | Week 12 | Week 16

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The Command Line, File Paths, Git

Week 1

• Topics:
  • Installing Software | Command-line | Git version control
• Assignments
  • Read: What is Git all about?
  • Install Git, R, and R-Studio on your laptop (part of Assignment 1)
  • Be ready to explain what Git, R, and R-Studio are.
  • Do Assignment 1 and upload a link to your new GitHub account to Canvas.
• Resources
  • Download Git
  • Download R
  • Download R-Studio
  • Navigating with the command line
  • Basic Git Commands
• Practice
  • Make 10 separate changes and commits to your README.md file and push each one to GitHub

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Week 2

• Topics
  • File paths | Pipes | Redirection | Wildcards | Essential Unix Commands | Parameters
• Assignments
  • Assignment 2
• Resources
  • Remedial Unix Shell
  • Basic Unix Commands
  • Very Useful Tutorial
• Practice
  • Exercise 1
  • Exercise 2

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Getting to Know R

Week 3

• Topics
  • R Data types and conversions | Reading and Writing Files | For-Loops | Packages and Projects
• Assignments
  • Assignment 3
  • Assignment 4
• Resources
  • Data Types in R
  • For-Loops
  • Reading data into R
  • R Projects
• Practice
  • Vectors
  • Factors
  • Characters
  • Regular Sequences
  • Indexing
  • Missing Values
  • Loops in R

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Week 4

• Topics
  • Logical Operations | Subsetting | “Grammar of Graphics” ggplot Intro
• Assignments
  • Read through the materials in the Resources section below
  • Assignment 5
  • Exam 1
• Resources
  • Subsetting
  • More Subsetting(It’s important!)
  • Operators
• Practice
  • Logical Operations
  • Find a new built-in data set in R. Use several methods to subset it over and over until you are an expert!
  • Out-of-order Code

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Visualizing a Data Set

Week 5

• Topics
  • ggplot | patchwork | ggforce
• Assignments
  • Assignment 6
  • Ugly plot contest!
• Resources
  • ggplot Introduction
  • More ggplot
  • ggforce
  • patchwork
  • Extensive ggplot2 Tutorial
• Practice
  • Out-of-order Plotting Code
  • ggplot Examples
  • ggplot Shiny App Lets you use GUI to see ggplot code.

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Clean and Transform Data

Week 6

• Topics
  • Tidy Data | dplyr verbs | tidyr verbs
• Assignments
  • Read this paper: Tidy Data
  • Assignment 7
• Resources
  • Tidy Data Chapter
  • Transforming Data Frames
  • dplyr Verbs
  • tidyr Verbs
  • tidyverse Cheat Sheet
• Practice
  • BioLog Challenge
  • Out-of-order Code
  • Out-of-order Code2

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Week 7

• Topics
  • Data Wrangling | Joins | The Curse of Other Peoples’ Data
• Assignments
  • Read This Handout
  • Read This Paper
  • Create a validated Excel Spreadsheet for data collection for the experiment we design in class
  • Exam 2
• Resources
  • Data Wrangling Chapter
  • Wrangling Cheat Sheet
  • Visual Explanations of Joins
• Practice
  • Download this spreadsheet. See if you figure out all the things wrong with it.
  • Error Sleuth Practice
  • Data Entry Case Study

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Getting More From R

Week 8

• Topics
  • Writing Functions | Conditional Execution | source()
• Assignments
• Resources
  • Functions
  • Conditional Execution
• Practice
  • Write a function that returns the min, max, and mean of any set of real numbers
  • Write a function that takes a data frame and returns a new data frame with one random column removed
  • Write a function that takes a data frame… if there are more than 3 columns, your function should return the column names as-is; if there are 3 or fewer columns, your function should return the column names in reverse order.
  • Write a useful function that you might want to use in the future (your choice)
  • Put all of these functions into a new R script and save it in your main data course repository
  • In a new empty R script, call your functions with source() and test them out

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Model Building and Testing

Week 9

• Topics
  • Building and Testing Models
• Assignments
  • Assignment 8
• Resources
  • Modeling Intro
  • Model Basics
  • Model Fitting
• Practice
  • Building Models Example
  • Intro to Hypothesis Testing
  • Cross-Validation and Logistic Regression

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Week 10

• Topics
  • More models | Statistical Tests
• Assignments
• Resources
  • Linear Regression
  • More Linear Regression
  • Common Statistical Tests
• Practice

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Communicating Your Results

Week 11

• Topics
  • R-Markdown | Reproducible Reports
• Assignments
  • Assignment 9
• Resources
  • Intro to R Markdown
  • Markdown Live Preview Generator
• Practice

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Week 12

• Topics
  • Proper Project Organization | Collaboration
• Assignments
  • Peer evaluation of Assignment 9 (Organization, Portability, Accuracy, Understandablity)
  • Exam 3
• Resources
  • Project-oriented Workflows
  • Reproducible, Portable, Self-Contained
  • Proper Project Organization Example
  • Another, More Detailed Example
• Practice

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Putting it all together

Week 13

• Topics
  • Data Analysis from raw to report
• Assignments
  • We will work together in class to do a complete analysis in real-time
• Resources
  • Benefits of Live Coding
• Practice
  • Analyze the “esoph” data set and generate a markdown report

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Week 14

• Topics
  • Building a website
• Assignments
  • Work on Final Project
  • Create a GitHub Personal Website
  • Upload a brief CV and the updated (improved) html of Assignment 9
• Resources
  • GitHub Pages
  • Here’s the GitHub repository for this entire website

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Week 15

• Topics -TBD
• Assignments
  • Work on Final Project

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Week 16

• Topics
  • TBD
• Assignments
  • Exam 4 (Redo any previous exam to replace it’s score)

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